From: fhh2626_at_gmail.com
Date: Tue Oct 04 2022 - 01:43:42 CDT
Hi, Joey,
Generally, you may want to read this paper (https://urldefense.com/v3/__https://www.nature.com/articles/s41596-021-00676-1__;!!DZ3fjg!5ewyr6eeyM_QLNQ6ApzQcZXC4nU8V7VyVsjF04vG3Q5CJ7za_5KDaNnBdV59pGt4RyYhC8klq4_JQo6b$ ) and use the automated tool for the task.
Regarding your question,
(1) You should reasonably set the range of the CVs to guarantee sufficient sampling of all bins. Otherwise the simulation may not be converged.
(2) In the unbound-state simulation, there should not be a harmonic restraint. See input files of step 8 generated by BFEE2.
(3) I do not understand the question. k can be an any value. The contribution of harmonic restraints, which is added one by one, will be calculated by post-treatments.
Best,
Haohao
fhh2626_at_gmail.com
From: Joey Farrell
Date: 2022-10-04 14:12
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: ABF Free Energy Calculation
Hello all,
I have three questions regarding how to properly use ABF to calculate Keq after reading the tutorial and searching the mailing list.
When calculating ∆G via discrete integral, should one only consider bins with a sufficient zcount, or ought all bins on the reaction coordinate contribute? If there is a minimum/threshold zcount, is it a function of the fullSamples parameter, or is it a general, approximate threshold?
In the ABF tutorial, the "unbound" state simulations have colvars which refer to the "bound" state structure as the reference structure. Should the centers of the harmonic restraints be updated such that there is no harmonic potential in frame 0 (i.e., an RMSD restraint originally with center 0 now has non-zero center since the reference structure is not itself)?
Each colvars forceConstant is only realized by a proceeding simulation (i.e., there is no value for "k" until the next colvar's simulation, which then uses the previous as a harmonic restraint). What, then, is the "k" value for the last colvar that is run, since it is by definition never used as a harmonic restraint in another colvar's simulation? It seems it cannot be the case that k=0, as inductively you would never need the last simulation (since ∆G contribution is 0 for k=0 in my understanding).
Thank you very much; I greatly appreciate any help with these questions.
Best,
Joey
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